DNABERT1 RefSeq400 Vs SpliceAI 400 on RefSeq400¶

In [1]:
from utility_transformers import plot_predictions_results_comapre, plot_predictions_results

nbins = 100

min_intron_length = 49
max_intron_length = 1100000

min_donor_length = 19
max_donor_length = 11000

min_acceptor_length = 19
max_acceptor_length = 11000

top_n_signals = 10
break_y_min, break_y_max, plotly_histogram_y, ystep = 50000, 50000, 350000, 50000

predictions_path_1          = "/data/SpliceUp/prediction/PREDICT__DNABERT1__RefSeq400/"
negative_predictions_path_1 = "/data/SpliceUp/prediction/PREDICT__DNABERT1__RefSeq400_Negative"

predictions_path_2          =  "/data/SpliceUp/prediction/spliceAI_refSeq400/"
negative_predictions_path_2 = "/data/SpliceUp/prediction/spliceAI_refSeq400_Negative/"

output_folder = "/data/SpliceUp/DeepSAP-main/scripts/plots/prediction/SpliceAI_vs_DNABERT1__RefSeq400_RefSeq400/"
pickled_junctions_path = "/data/SpliceUp/pickles/not_strict_annotated_junctions_table__RefSeq__400.pkl"

plot_predictions_results_comapre(pickled_junctions_path, predictions_path_1, negative_predictions_path_1, predictions_path_2, negative_predictions_path_2, output_folder, "DNABERT1 RefSeq400", "SpliceAI 400", "RefSeq400", break_y_min, break_y_max, plotly_histogram_y, ystep, nbins, min_intron_length, max_intron_length, min_donor_length, max_donor_length, min_acceptor_length, max_acceptor_length, top_n_signals, is_show_legend=True)
Plotting scores vs intron length
Plotting scores vs acceptor and donor length
Plotting violins of scores per bitype and signal 
No description has been provided for this image
No description has been provided for this image
No description has been provided for this image

DNABERTT MS150 vs DNABERT1 RefSeq150 on RefSeq150¶

In [2]:
from utility_transformers import plot_predictions_results_comapre

nbins = 100

min_intron_length = 49
max_intron_length = 1100000

min_donor_length = 19
max_donor_length = 11000

min_acceptor_length = 19
max_acceptor_length = 11000

top_n_signals = 10
break_y_min, break_y_max, plotly_histogram_y, ystep = 50000, 50000, 350000, 50000

predictions_path_1          = "/data/SpliceUp/prediction/PREDICT__DNABERT1__RefSeq150/"
negative_predictions_path_1 = "/data/SpliceUp/prediction/PREDICT__DNABERT1__RefSeq150_Negative/"

predictions_path_2          = "/data/SpliceUp/prediction/PREDICT__DNABERT1__MultiSpecies150_RefSeq150/"
negative_predictions_path_2 = "/data/SpliceUp/prediction/PREDICT__DNABERT1__MS150__RefSeq150_Negative/"

output_folder = "/data/SpliceUp/DeepSAP-main/scripts/plots/prediction/DNABERT1__MS150_vs_DNABERT1__RefSeq150_RefSeq150/"
pickled_junctions_path = "/data/SpliceUp/pickles/not_strict_annotated_junctions_table__RefSeq__150.pkl"

plot_predictions_results_comapre(pickled_junctions_path, predictions_path_1, negative_predictions_path_1, predictions_path_2, negative_predictions_path_2, output_folder, "DNABERT1 RefSeq150", "DNABERT1 MS150", "RefSeq150", break_y_min, break_y_max, plotly_histogram_y, ystep, nbins, min_intron_length, max_intron_length, min_donor_length, max_donor_length, min_acceptor_length, max_acceptor_length, top_n_signals, is_show_legend=True)
Plotting scores vs intron length
Plotting scores vs acceptor and donor length
Plotting violins of scores per bitype and signal 
No description has been provided for this image
No description has been provided for this image
No description has been provided for this image

DNABERTT MS150 vs DNABERT1 PF150 on PF150¶

In [3]:
from utility_transformers import plot_predictions_results_comapre, plot_predictions_results

nbins = 100

min_intron_length = 0
max_intron_length = 110000

min_donor_length = 0
max_donor_length = 11000

min_acceptor_length = 0
max_acceptor_length = 11000

top_n_signals = 10
plotly_histogram_y = 8000

predictions_path_1          = "/data/SpliceUp/prediction/PREDICT__DNABERT1_k6__Splice__PF_r57_150/"
negative_predictions_path_1 = "/data/SpliceUp/prediction/PREDICT__DNABERT1__PF_r57_150_Negative/"

predictions_path_2          = "/data/SpliceUp/prediction/PREDICT__DNABERT1__MultiSpecies150_PF_r57_150/"
negative_predictions_path_2 = "/data/SpliceUp/prediction/PREDICT__DNABERT1__MS150__PF_r57_150_Negative/"

output_folder = "/data/SpliceUp/DeepSAP-main/scripts/plots/prediction/DNABERT1__MS150_vs_DNABERT1__PF150_PF150/"
pickled_junctions_path = "/data/SpliceUp/pickles/not_strict_annotated_junctions_table__PF_r57__150.pkl"

top_n_signals = 10
# break_y_min, break_y_max, plotly_histogram_y = 20000, 1001, 10000
break_y_min, break_y_max, plotly_histogram_y, ystep = 1000, 1000, 10000, 2000

plot_predictions_results_comapre(pickled_junctions_path, predictions_path_1, negative_predictions_path_1, predictions_path_2, negative_predictions_path_2, output_folder, "DNABERT1 Malaria150", "DNABERT1 MS150", "Malria150", break_y_min, break_y_max, plotly_histogram_y, ystep, nbins, min_intron_length, max_intron_length, min_donor_length, max_donor_length, min_acceptor_length, max_acceptor_length, top_n_signals, is_show_legend=True)

# plot_predictions_results_comapre(pickled_junctions_path, predictions_path_1, negative_predictions_path_1, predictions_path_2, negative_predictions_path_2, output_folder, "DNABERT1 Malaria150", "DNABERT1 MS150", "Malria150",plotly_histogram_y, nbins, min_intron_length, max_intron_length, min_donor_length, max_donor_length, min_acceptor_length, max_acceptor_length, top_n_signals, is_show_legend=True, plotly_histogram_y=8000)
Plotting scores vs intron length
Plotting scores vs acceptor and donor length
Plotting violins of scores per bitype and signal 
No description has been provided for this image
No description has been provided for this image
No description has been provided for this image